Franklin Richards is having a nightmare wherein his father Reed Richards has killed his mother Sue. Reed tells young Franklin to go away, that it was necessary. To Franklin's continued horror, the other members of the Fantastic Four are dead as well. Not only that, but Wolverine appears carrying the dead body of Shadowcat and tells young Franklin that his father not only killed the Fantastic Four but his allies in the X-Men as well. When Wolverine attempts to kill Reed Richards, he collapses due to his own wounds and dies, missing the chance to land a fatal blow on Reed. As Reed carries the lifeless body of his wife up a flight of stairs, Franklin tries to follow begging his father to turn back and go with him. However, he continues to ignore the boys pleas and puts her body on an altar. There he finds a book labeled "Reed Richards Journal, State University". Franklin begs his father not to open the book, but his cries go unheard as Reed opens the book and it transforms him, making him evil. Tearing off his Fantastic Four costume Reed reveals that he is wearing the garb of Dr. Doom underneath and places a red-hot mask over his face. He tells his son that his father and his father's greatest enemy are one.

With this Franklin wakes up with a scream. Going to check on his father, Franklin finds him working in his lab. When Franklin tries to tell his father about his dream, he ignores the boy and calls Sue who pulls the boy into another room where she is busy unpacking crates of items moved from Avengers Mansion to the Fantastic Four's new headquarters the Four Freedoms Plaza. When Sue learns that Franklin is up past his bedtime due to one of his special dreams, she comforts the boy and then resumes unpacking crates. When she finds one containing items that have been in storage since before Sue and Reed were married, Sue goes digging through and finds the notebook from Franklin's dream inside. Recognizing it Franklin is frightened by it and tells her not to give it to his father.

Meanwhile, on Muir Island, Alex Summers goes to see if Rogue needs a hand working maintenance on the Blackbird. When Rogue snubs him, Alex tries to pull seniority on her and she tells him that the X-Men have changed since he was last a member and tells him that he has to earn his place with the team. While elsewhere on the facility Colossus, and Nightcrawler are still recovering from injuries sustained during the Mutant Massacre[1]. While Shadowcat is not getting any better, her disrupted molecules are drifting further and further apart to the point where it will be only a matter of days before it causes irreparable brain damage. Kitty is so far gone at this point that she can only communicate telepathically with Psylocke. While Moira MacTaggert is telling Storm and Wolverine the prognosis Magneto contacts them from the States to tell them that he has learned that Reed Richards of the Fantastic Four has come up with a device that might be able reverse Kitty's condition and that he will attempt to contact the Fantastic Four, even though Storm is concerned that the group may still consider Magneto a villain. While out at sea near Muir Island, Dazzler and Longshot are spending the day tooling around the waters by boat. As they motor along Longshot detects something in the water and dives in, much to Alison's shock. Because it is dark out, she uses her powers to illuminate the area and is surprised to find that Longshot found someone who was lost out at sea. They pull him aboard, and when they tell him the man that they are taking him back to Muir Island, the man smiles.

Back at the Four Freedoms Plaza, Sue has put Franklin to bed and has begun browsing Reed's old journal, and she has become terribly upset by what she has read. Franklin's dream self appears in the room to watch as Reed enters the room to and tries to surprise his wife. However, she has a surprise for him: She read a passage in his book where it appears that Reed stated that he purposely neglected to shield the rocket ship before the accident that turned them into the Fantastic Four. This revelation shocks both Reed and young Franklin as well.

In Greenwich Village, at Raglan's Coffee House, She-Hulk is spending her evening studying over law books when she sniffs the reek of cigar smoke. Looking around the corner she is surprised to find Ben Grimm reading over Federal aviation manuals. Ben learns that Jennifer has gone back to lawyering on weekends, and Ben tells her that he has to get re-certified by the FAA. Ben brings up the recent trail on Magneto, and opinions that he'd rather quit than defend the mutant terrorist. She-Hulk however doesn't feel so strongly, telling Ben that she believes that everyone deserves a fair trail. Just then there is an explosion and the two look out the window to see that the source is at a nearby construction site. Springing into action, the two heroes brace the collapsing girders however it is not until the timely arrival of Magneto does the disaster get averted when the Master of Magnetism uses his powers to righten the building. When the Human Torch arrives, Magneto tells the young FF member to use his flame powers to weld the girders back in place. Johnny goes about doing so although he is shocked to believe that Magneto is giving him orders to help people.

With the crisis averted, Magneto accompanies the other members back to the Four Freedoms Plaza where he requests audience from Reed Richards. Confined to an invisible force field, Magneto pleads his case, telling him about Shadowcat's plight. Reed, shaken by the finding of his old journal doesn't think it's the right time, but Johnny presses him into going. When he tries to explain it to Sue, Sue angrily tells him that there is always a life at stake when they are having problems and tells him to go, that she will still be at headquarters when he gets back. Although deep down she wonders what will become of their family. Later, Reed, Ben, Johnny and She-Hulk (who has tagged along out of curiosity even though she left the FF to rejoin the Avengers)take the Fantastic Four's super-sonic jet to Muir Island with Magneto to see what they can do about Kitty Pryde.

On the flight over, the deeply troubled Richards asks Ben if he thinks that he is reckless or ruthless. Ben doesn't think so and reassures Reed that he handles every problem from every conceivable angle. He affirms to Reed that he is always right, but jests that the only time he made a mistake was the day they all got their powers and wonders how someone as smart as Reed could have overlooked the risk Cosmic Rays played in their space trip. This off the cuff remark worries Reed even deeper.

Soon, when the Fantastic Four arrive on Muir Island, Magneto is reunited with his X-Men comrades while She-Hulk and Thing unload Reed's device off the ship. Inside, Reed considers what Ben said, and Sue's anger and wonders if he did purposely mutate his comrades in the name of science. Wondering if perhaps he is reckless, and soon begins to doubt himself. As Reed exits the ship, Franklin's dream form appears and begins watching the proceeding events. As Reed walks by, he wonders how the X-Men can have faith in him when he has no faith in himself. As he walks by, Johnny, Magneto, Storm and Wolverine all notice something wrong with Reed. When Reed meets with Moira MacTaggert, he tells her there is nothing he can do. This angers Magneto who challenges Richard's claim saying that he papers released on his molecular bonding process were a success. However Reed tells Magneto that it has never been tested on a living being and isn't sure if it will work.

Realizing that Richards is afraid, Magneto uses his powers to snatch the device out of the Thing and She-Hulk's hands, but the She-Hulk pinches his hand breaking his concentration causing the device to drop back in the Thing's arms. With a fight about to break out, the Human Torch tries to flame on into action and is sucker punched by Wolverine who knocks the wind out of him. Wolverine then extracts his claws and charge at Mr. Fantastic he comes up close and tells Richards that they count on him to save Shadowcat's life, and orders him to save her life... Or die.

The Invisible Woman states that it was "ages" ago when she and Mister Fantastic got married. They were married in Fantastic Four Annual #3. Per the Sliding Timescsale of Earth-616 it has been roughly seven years between Reed and Sue's wedding and this story.

She-Hulk is still technically a member of the Fantastic Four after joining the team in Fantastic Four #265 even after the Thing returned in Fantastic Four #296. This adventure marks her last official outing with the team as an in-uniform member.

The Fantastic Four are not ready to trust Magneto because when they last encountered him in Marvel Super Heroes Secret Wars #1-12 he was still an enemy of the human race. They are unaware that Magneto recently renounced his ways and joined up with the X-Men back in Uncanny X-Men #200.